Package evaluation of MendelImpute on Julia 1.11.4 (a71dd056e0*) started at 2025-04-09T01:23:12.130 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.36s ################################################################################ # Installation # Installing MendelImpute... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [e47305d1] + MendelImpute v1.2.6 Updating `~/.julia/environments/v1.11/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [7d9fca2a] + Arpack v0.5.4 [4fba245c] + ArrayInterface v7.18.0 [4c555306] + ArrayLayouts v1.11.1 ⌅ [67c07d97] + Automa v0.8.4 [13072b0f] + AxisAlgorithms v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [fbb218c0] + BSON v0.3.9 [47718e42] + BioGenerics v0.1.5 [d1d4a3ce] + BitFlags v0.1.9 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.6 [336ed68f] + CSV v0.10.15 [d360d2e6] + ChainRulesCore v1.25.1 [fb6a15b2] + CloseOpenIntervals v0.1.13 [aaaa29a8] + Clustering v0.15.8 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.6 [35d6a980] + ColorSchemes v3.29.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.0 [861a8166] + Combinatorics v1.0.2 [38540f10] + CommonSolve v0.2.4 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [f0e56b4a] + ConcurrentUtilities v2.5.0 [187b0558] + ConstructionBase v1.5.8 [d38c429a] + Contour v0.6.3 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.118 [ffbed154] + DocStringExtensions v0.9.4 [460bff9d] + ExceptionUnwrapping v0.1.11 [c87230d0] + FFMPEG v0.4.2 [7a1cc6ca] + FFTW v1.8.1 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [53c48c17] + FixedPointNumbers v0.8.5 [1fa38f19] + Format v1.3.7 [28b8d3ca] + GR v0.73.13 [c27321d9] + Glob v1.3.1 [42e2da0e] + Grisu v1.0.2 [d853e229] + GroupSlices v0.0.3 [cd3eb016] + HTTP v1.10.15 [3e5b6fbb] + HostCPUFeatures v0.1.17 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.5 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.3 [a98d9a8b] + Interpolations v0.15.1 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 ⌅ [033835bb] + JLD2 v0.4.54 [1019f520] + JLFzf v0.1.10 [692b3bcd] + JLLWrappers v1.7.0 [9da8a3cd] + JLSO v2.7.0 [682c06a0] + JSON v0.21.4 [5ab0869b] + KernelDensity v0.6.9 [b964fa9f] + LaTeXStrings v1.4.0 [23fbe1c1] + Latexify v0.16.7 [10f19ff3] + LayoutPointers v0.1.17 ⌅ [5078a376] + LazyArrays v1.10.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.1.0 [bdcacae8] + LoopVectorization v0.12.172 [1914dd2f] + MacroTools v0.5.15 [d125e4d3] + ManualMemory v0.1.8 ⌅ [a3b82374] + MatrixFactorizations v2.2.0 [739be429] + MbedTLS v1.1.9 [442fdcdd] + Measures v0.3.2 [f28f55f0] + Memento v1.4.1 [e47305d1] + MendelImpute v1.2.6 [e1d29d7a] + Missings v1.2.0 [6f286f6a] + MultivariateStats v0.10.3 [77ba4419] + NaNMath v1.1.3 [b8a86587] + NearestNeighbors v0.4.21 [510215fc] + Observables v0.5.5 [6fe1bfb0] + OffsetArrays v1.16.0 [4d8831e6] + OpenSSL v1.4.3 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.33 [69de0a69] + Parsers v2.8.1 [ccf2f8ad] + PlotThemes v3.3.0 [995b91a9] + PlotUtils v1.4.3 [91a5bcdd] + Plots v1.40.11 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [c84ed2f1] + Ratios v0.4.5 [3cdcf5f2] + RecipesBase v1.3.4 [01d81517] + RecipesPipeline v0.6.12 [189a3867] + Reexport v1.2.2 [05181044] + RelocatableFolders v1.0.1 [ae029012] + 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[5c2747f8] + URIs v1.5.2 [3a884ed6] + UnPack v1.0.2 [1cfade01] + UnicodeFun v0.4.1 [1986cc42] + Unitful v1.22.0 [45397f5d] + UnitfulLatexify v1.6.4 [41fe7b60] + Unzip v0.2.0 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.6 [3d5dd08c] + VectorizationBase v0.21.71 [ea10d353] + WeakRefStrings v1.4.2 [cc8bc4a8] + Widgets v0.6.7 [efce3f68] + WoodburyMatrices v1.0.0 [76eceee3] + WorkerUtilities v1.6.1 ⌅ [68821587] + Arpack_jll v3.5.1+1 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.4+0 [ee1fde0b] + Dbus_jll v1.16.2+0 [2702e6a9] + EpollShim_jll v0.0.20230411+1 [2e619515] + Expat_jll v2.6.5+0 ⌅ [b22a6f82] + FFMPEG_jll v4.4.4+1 [f5851436] + FFTW_jll v3.3.11+0 [a3f928ae] + Fontconfig_jll v2.16.0+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [559328eb] + FriBidi_jll v1.0.17+0 [0656b61e] + GLFW_jll v3.4.0+2 [d2c73de3] + GR_jll v0.73.13+0 [78b55507] + Gettext_jll v0.21.0+0 ⌃ [7746bdde] + Glib_jll v2.82.4+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.0+0 [1d5cc7b8] + IntelOpenMP_jll v2025.0.4+0 [aacddb02] + JpegTurbo_jll v3.1.1+0 [c1c5ebd0] + LAME_jll v3.100.2+0 [88015f11] + LERC_jll v4.0.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.7+0 [dd4b983a] + LZO_jll v2.10.3+0 ⌅ [e9f186c6] + Libffi_jll v3.2.2+2 [d4300ac3] + Libgcrypt_jll v1.11.1+0 [7e76a0d4] + Libglvnd_jll v1.7.0+0 [7add5ba3] + Libgpg_error_jll v1.51.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.0+0 [89763e89] + Libtiff_jll v4.7.1+0 [38a345b3] + Libuuid_jll v2.41.0+0 [856f044c] + MKL_jll v2025.0.1+1 [e7412a2a] + Ogg_jll v1.3.5+1 [458c3c95] + OpenSSL_jll v3.0.16+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [91d4177d] + Opus_jll v1.3.3+0 [36c8627f] + Pango_jll v1.56.1+0 [30392449] + Pixman_jll v0.44.2+0 ⌅ [c0090381] + Qt6Base_jll v6.7.1+1 ⌅ [629bc702] + Qt6Declarative_jll v6.7.1+2 ⌅ [ce943373] + Qt6ShaderTools_jll v6.7.1+1 ⌃ [e99dba38] + Qt6Wayland_jll v6.7.1+1 [f50d1b31] + Rmath_jll v0.5.1+0 [76ed43ae] + SQLite_jll v3.48.0+0 [a44049a8] + Vulkan_Loader_jll 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Xorg_xcb_util_renderutil_jll v0.3.9+1 [c22f9ab0] + Xorg_xcb_util_wm_jll v0.4.1+1 [35661453] + Xorg_xkbcomp_jll v1.4.6+1 [33bec58e] + Xorg_xkeyboard_config_jll v2.39.0+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 [35ca27e7] + eudev_jll v3.2.9+0 [214eeab7] + fzf_jll v0.56.3+0 [1a1c6b14] + gperf_jll v3.1.1+1 [a4ae2306] + libaom_jll v3.11.0+0 [0ac62f75] + libass_jll v0.15.2+0 [1183f4f0] + libdecor_jll v0.2.2+0 [2db6ffa8] + libevdev_jll v1.11.0+0 [f638f0a6] + libfdk_aac_jll v2.0.3+0 [36db933b] + libinput_jll v1.18.0+0 [b53b4c65] + libpng_jll v1.6.47+0 [f27f6e37] + libvorbis_jll v1.3.7+2 [009596ad] + mtdev_jll v1.1.6+0 [1317d2d5] + oneTBB_jll v2022.0.0+0 ⌅ [1270edf5] + x264_jll v2021.5.5+0 ⌅ [dfaa095f] + x265_jll v3.5.0+0 [d8fb68d0] + xkbcommon_jll v1.4.1+2 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.11.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [efcefdf7] + PCRE2_jll v10.42.0+1 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 5.12s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 121.53s ################################################################################ # Testing # Testing MendelImpute Status `/tmp/jl_cLkUfg/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.0 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [b4f34e82] Distances v0.10.12 [5789e2e9] FileIO v1.17.0 [53c48c17] FixedPointNumbers v0.8.5 [d853e229] GroupSlices v0.0.3 ⌅ [033835bb] JLD2 v0.4.54 [9da8a3cd] JLSO v2.7.0 ⌅ [5078a376] LazyArrays v1.10.0 [e47305d1] MendelImpute v1.2.6 [92933f4c] ProgressMeter v1.10.4 [4e780e97] SnpArrays v0.3.22 [276daf66] SpecialFunctions v2.5.0 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.4 [f3b207a7] StatsPlots v0.15.7 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [37e2e46d] LinearAlgebra v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_cLkUfg/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [7d9fca2a] Arpack v0.5.4 [4fba245c] ArrayInterface v7.18.0 [4c555306] ArrayLayouts v1.11.1 ⌅ [67c07d97] Automa v0.8.4 [13072b0f] AxisAlgorithms v1.1.0 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [fbb218c0] BSON v0.3.9 [6e4b80f9] BenchmarkTools v1.6.0 [47718e42] BioGenerics v0.1.5 [d1d4a3ce] BitFlags v0.1.9 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] BufferedStreams v1.2.2 [2a0fbf3d] CPUSummary v0.2.6 [336ed68f] CSV v0.10.15 [d360d2e6] ChainRulesCore v1.25.1 [fb6a15b2] CloseOpenIntervals v0.1.13 [aaaa29a8] Clustering v0.15.8 [523fee87] CodecBzip2 v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.6 [35d6a980] ColorSchemes v3.29.0 [3da002f7] ColorTypes v0.12.1 [c3611d14] ColorVectorSpace v0.11.0 [5ae59095] Colors v0.13.0 [861a8166] Combinatorics v1.0.2 [38540f10] CommonSolve v0.2.4 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.16.0 [a33af91c] CompositionsBase v0.1.2 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Test Summary: | Pass Total Time search breakpoints | 8 8 1.6s Test Summary: | Pass Total Time intersect code | 9 9 0.9s Test Summary: | Pass Total Time dynamic programming | 10 10 4.8s ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 importing reference data... 27%|██████▍ | ETA: 0:00:14 importing reference data... 57%|█████████████▋ | ETA: 0:00:10 importing reference data... 86%|████████████████████▌ | ETA: 0:00:03 importing reference data... 100%|████████████████████████| Time: 0:00:22 102.433422 seconds (187.84 M allocations: 16.352 GiB, 2.90% gc time, 65.28% compilation time: <1% of which was recompilation) 6.878007 seconds (3.55 M allocations: 173.762 MiB, 0.57% gc time, 96.76% compilation time) Test Summary: | Pass Total Time compress | 11 11 1m49.4s Number of threads = 1 Importing reference haplotype data... Computing optimal haplotypes... 12%|██▌ | ETA: 0:03:02 Computing optimal haplotypes... 100%|████████████████████| Time: 0:00:28 Phasing... 2%|▉ | ETA: 0:04:41 Phasing... 100%|█████████████████████████████████████████| Time: 0:00:08 Total windows = 16, averaging ~ 708 unique haplotypes per window. Timings: Data import = 1.95802 seconds import target data = 1.73356 seconds import compressed haplotypes = 0.224459 seconds Computing haplotype pair = 31.0624 seconds BLAS3 mul! to get M and N = 0.166557 seconds per thread haplopair search = 2.92969 seconds per thread initializing missing = 0.0124707 seconds per thread allocating and viewing = 0.0425305 seconds per thread index conversion = 0.000125239 seconds per thread Phasing by win-win intersection = 9.6731 seconds Window-by-window intersection = 0.00337952 seconds per thread Breakpoint search = 4.16641 seconds per thread Recording result = 0.00124153 seconds per thread Imputation = 7.86896 seconds Imputing missing = 3.9294 seconds Writing to file = 3.93956 seconds Total time = 50.8108 seconds 50.891554 seconds (46.34 M allocations: 2.363 GiB, 2.38% gc time, 89.43% compilation time) Test Summary: | Pass Total Time impute & phasing | 10 10 1m32.8s Number of threads = 1 Importing reference haplotype data... Total windows = 16, averaging ~ 708 unique haplotypes per window. Timings: Data import = 0.764357 seconds import target data = 0.556342 seconds import compressed haplotypes = 0.208015 seconds Computing haplotype pair = 3.86094 seconds BLAS3 mul! to get M and N = 0.195804 seconds per thread haplopair search = 3.45305 seconds per thread initializing missing = 0.0143059 seconds per thread allocating and viewing = 0.0534502 seconds per thread index conversion = 0.000124099 seconds per thread Phasing by win-win intersection = 0.366146 seconds Window-by-window intersection = 0.00299074 seconds per thread Breakpoint search = 0.218055 seconds per thread Recording result = 0.00085414 seconds per thread Imputation = 0.925949 seconds Imputing missing = 0.0905709 seconds Writing to file = 0.835378 seconds Total time = 5.9181 seconds 5.918496 seconds (2.05 M allocations: 186.647 MiB, 0.77% gc time) Number of threads = 1 Importing reference haplotype data... Total windows = 16, averaging ~ 708 unique haplotypes per window. Timings: Data import = 4.04786 seconds import target data = 3.8073 seconds import compressed haplotypes = 0.240559 seconds Computing haplotype pair = 3.22267 seconds BLAS3 mul! to get M and N = 0.168591 seconds per thread haplopair search = 2.85145 seconds per thread initializing missing = 0.0142366 seconds per thread allocating and viewing = 0.0422169 seconds per thread index conversion = 0.000118389 seconds per thread Phasing by win-win intersection = 0.346537 seconds Window-by-window intersection = 0.00313674 seconds per thread Breakpoint search = 0.192739 seconds per thread Recording result = 0.00114999 seconds per thread Imputation = 1.958 seconds Imputing missing = 0.07061 seconds Writing to file = 1.88739 seconds Total time = 9.57568 seconds 9.575819 seconds (1.88 M allocations: 139.185 MiB, 0.33% gc time, 51.29% compilation time) Number of threads = 1 Importing reference haplotype data... Computing optimal haplotypes... 81%|████████████████▎ | ETA: 0:00:01 Computing optimal haplotypes... 100%|████████████████████| Time: 0:00:05 Phasing... 22%|█████████ | ETA: 0:00:20 Phasing... 100%|█████████████████████████████████████████| Time: 0:00:05 Total windows = 16, averaging ~ 708 unique haplotypes per window. Timings: Data import = 2.2732 seconds import target data = 2.0292 seconds import compressed haplotypes = 0.243991 seconds Computing haplotype pair = 6.04755 seconds BLAS3 mul! to get M and N = 0.162161 seconds per thread haplopair search = 2.74886 seconds per thread initializing missing = 0.0127802 seconds per thread allocating and viewing = 0.0405283 seconds per thread index conversion = 0.000127338 seconds per thread Phasing by win-win intersection = 6.20045 seconds Window-by-window intersection = 0.00304154 seconds per thread Breakpoint search = 3.5916 seconds per thread Recording result = 0.00122392 seconds per thread Imputation = 3.50291 seconds Imputing missing = 2.71434 seconds Writing to file = 0.788563 seconds Total time = 18.0377 seconds 18.037808 seconds (6.80 M allocations: 363.446 MiB, 0.85% gc time, 70.14% compilation time) Test Summary: | Pass Total Time PLINK and dosage inputs | 2 2 38.3s Number of threads = 1 Importing reference haplotype data... Total windows = 16, averaging ~ 708 unique haplotypes per window. Timings: Data import = 0.740768 seconds import target data = 0.503258 seconds import compressed haplotypes = 0.23751 seconds Computing haplotype pair = 3.36639 seconds BLAS3 mul! to get M and N = 0.167663 seconds per thread haplopair search = 3.01068 seconds per thread initializing missing = 0.0128424 seconds per thread allocating and viewing = 0.0474363 seconds per thread index conversion = 0.00012651 seconds per thread Phasing by win-win intersection = 1.53525 seconds Window-by-window intersection = 0.00318641 seconds per thread Breakpoint search = 0.178588 seconds per thread Recording result = 0.000236076 seconds per thread Imputation = 3.02687 seconds Imputing missing = 4.90915e-5 seconds Writing to file = 3.02682 seconds Total time = 8.66983 seconds 8.670114 seconds (3.69 M allocations: 229.754 MiB, 0.49% gc time, 48.71% compilation time) importing reference data... 31%|███████▌ | ETA: 0:00:11 importing reference data... 62%|███████████████ | ETA: 0:00:06 importing reference data... 95%|██████████████████████▋ | ETA: 0:00:01 importing reference data... 100%|████████████████████████| Time: 0:00:15 Test Summary: | Pass Total Time decompress ultra-compressed files | 1 1 32.1s Test Summary: | Pass Total Time 0 allocations in phasing | 2 2 7.0s Test Summary: | Pass Total Time 0 allocation in haplopair | 2 2 17.1s import BGEN: Error During Test at /home/pkgeval/.julia/packages/MendelImpute/z2M6N/test/runtests.jl:316 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] decompress @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:42 [inlined] [5] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [6] first_allele_dosage! @ ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:549 [inlined] [7] convert_gt(t::Type{Float64}, b::Bgen) @ MendelImpute ~/.julia/packages/MendelImpute/z2M6N/src/read.jl:38 [8] macro expansion @ ./timing.jl:581 [inlined] [9] macro expansion @ ~/.julia/packages/MendelImpute/z2M6N/test/runtests.jl:318 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [11] top-level scope @ ~/.julia/packages/MendelImpute/z2M6N/test/runtests.jl:318 [12] include(fname::String) @ Main ./sysimg.jl:38 [13] top-level scope @ none:6 [14] eval @ ./boot.jl:430 [inlined] [15] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [16] _start() @ Base ./client.jl:531 Test Summary: | Error Total Time import BGEN | 1 1 1.5s ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MendelImpute/z2M6N/test/runtests.jl:316 Testing failed after 423.36s ERROR: LoadError: Package MendelImpute errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 573.4s: package tests unexpectedly errored